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Kyoto Encyclopedia of Genes and Genomes (KEGG)
Biomolecular Reaction pathways for Information Transfer and Expression (BRITE)
Signaling PAthway Database (SPAD)
Cell Signaling Networks Database (CSNDB)
WIT2 - What Is There
Biocatalysis/Biodegradation Database
Boehringer Mannheim - Biochemical pathways database
ExPASy Biochemical Pathways
Klotho: Biochemical Compounds Declarative Database
Muscle-Specific Regulation of Transcription
GBF - Molecular Bioinformatics of Gene Regulation
TRANSFAC - Transcription Factor database
GeNet - Gene Networks Data Base
GeneNet - Computing System for Automated Gene Network Visualisation
MMP - Main Metabolic Pathways
FlyNets-Interactilist - Direct molecular interactions in Drosophila
The Organ Development Database
Gene expression in tooth (TOOTHEXP)
EpoDB - Erythropoiesis Database
Kyoto Encyclopedia of Genes and Genomes (KEGG)
This is an attempt to computerize current knowledge of molecular and
cellular biology in terms of the information pathways that consist of
interacting genes and molecules.
KEGG is composed of three interconnected sections: genes, molecules, and pathways, which are also linked to a number of existing databases through our DBGET retrieval system. The genes section contains a functionally classified table of genes for each organism. The classification is based on the pathway section, which contains a number of diagrams representing the flow of information in all known aspects of biological functions. At the moment we are just working on the metabolic pathways. The molecules section also contains classified tables of proteins, RNAs, small molecules, and molecular assemblies.
Biomolecular Reaction pathways for Information Transfer and Expression (BRITE)
This is a graphical database for several species of the biochemical
pathways involved in expression and controlling cell cycles.
Signaling PAthway Database (SPAD)
SPAD is classified into four categories based on extracellular
signal molecule (Growth factor, Cytokine, Hormone and Stress) that
initiate the intracellular signaling pathway. SPAD holds
information on interaction between protein and protein, protein and DNA
as well as the sequence (DNA and protein).
Cell Signaling Networks Database (CSNDB)
CSNDB is a data and knowledge base for cellular signal
transduction for human.
WIT2 - What Is There
The WIT system helps users create metabolic reconstructions, which is
made possible by the recent abundance of complete bacterial genomic
sequences. Such reconstructions will for the first time set the stage
for meaningful simulations of the basic behaviour of microbes, and may
thus significantly advance microbial biology.
The characterization of unicellular life, a scientific endeavor being increasingly driven by large-scale sequencing efforts, is reshaping biology. It is fundamental research that will ultimately be the fountainhead of both insights and applications. The availability of complete genomes is setting the stage for advances and integrations in our understanding of microbial biochemistry and genetics.
Biocatalysis/Biodegradation Database
Microbial biocatalytic reactions and biodegradation pathways primarily
for xenobiotic, chemical compounds.
Boehringer Mannheim - Biochemical pathways database
A search for an enzyme name results in a list of links to the ENZYME Database and, for each entry, links to all maps of "Biochemical
Pathways" in which this entry appears.
ExPASy Biochemical Pathways
This is a searchable database of the Biochemical Pathways" index of
Boehringer Mannheim.
Klotho: Biochemical Compounds Declarative Database
Klotho is part of an attempt to model biological processes, beginning with biochemistry.
Muscle-Specific Regulation of Transcription
This site presents a summary of published information on muscle-specific
transcriptional regulation. Eventually they hope to include all genes
known to be either up- or down-regulated in any type of muscle tissue.
The current short term goal is to include all genes known to be
up-regulated in skeletal muscle.
GBF - Molecular Bioinformatics of Gene Regulation
The GBF project "Molecular Bioinformatics of Gene Regulation" deals with
the DNA sequence features of regulatory genomic elements and regions, in
particular those that govern transcriptional control. The project
comprises theroretical as well as experimental work. The basis of the
theoretical part is the TRANSFAC database. It compiles data about gene
regulatory DNA sequences and protein factors binding to them. On this
basis, programs are developed that help to identify putative promoter or
enhancer structures and to suggest their features. These efforts are
part of ring funding projects GENUS (GEne regulatory NUcleic acid
Sequences) financed by the BMBF (the previous BMFT) and TRADAT
(TRAnscription DATabases and analysis tools) by the European Comission.
TRANSFAC - Transcription Factor database
TRANSFAC is a database on eukaryotic cis-acting regulatory DNA
elements and trans-acting factors. It covers the whole range from yeast to
human.
The first criterion for a site to be included in TRANSFAC is protein binding, the second is function. Assigned to each site is an unambiguous accession number and an identifier. The latter is composed of a hint onto the species (e. g., HS for human), a code for the gene description and a consecutive number for each entry referring to a particular gene. Thus, HS$BAC_2 refers to the 2nd entry for the human gene for beta-actin.
GeNet - Gene Networks Data Base
The database presents known gene networks organization.
It include maps of gene-gene interactions,
sequences and structure of known regulatory
elements, links to GenBank and Medline references.
GENET is aimed at exploration of areas that are not covered completely by other DBs on gene regulation (EPD, TRRD, COMPEL).
GeneNet - Computing System for Automated Gene Network Visualisation
A program for automated visualization of the gene network based on experimental information presented
in standard format in the GeneNet database.
The regulation of two biological functions antiviral response and hematopoiesis is described in the GeneNet. Gene interdependence, signal transduction pathways and the major features of gene network operation are described for each function. A program provision in Java makes possible automated construction of gene network diagrams.
MMP - Main Metabolic Pathways
A diagram of the main metabolic pathways.
FlyNets-Interactilist - Direct molecular interactions in Drosophila
This contains a preliminary list of molecular interactions occuring in
Drosophila melanogaster. For each one of them, it has been "reasonnably" proven
experimentally (at least one in vivo and one in vitro experiment) that a direct
interaction does indeed occur between two molecular partners.
All interactions described in Interactilist are classified according to their molecular nature which could be either Protein-DNA, Protein-RNA or Protein-protein.
The Organ Development Database
The Organ Development Database exists to summarise information about gene expre$
phenotypes in a number of developing mammalian glandular organs. Some parts of $
fully functional; others are under construction.
Gene expression in tooth (TOOTHEXP)
Information about expression of different genes in the developing tooth.
The aim is to provide a useful tool for learning and comparing the
expression patterns of different genes and detecting coexpression. For
this purpose a graphical form of presentation is provided where
available.
EpoDB - Erythropoiesis Database
A database of genes that relate to vertebrate red blood cells.
It includes DNA sequence, structural features and potential
transcription factor binding sites.
Any Comments, Questions? Support@hgmp.mrc.ac.uk
